<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

! Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and Ethics Program, University of Pittsburgh)

General Formatting

• Manuscripts should generally be double spaced throughout.
• Don't format with multiple columns.
• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
• Don't indent the first paragraph after a heading.
• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• Use Zotero to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• Be sure you are using standard journal abbreviations. You can find them by Googling and looking for: "Abbreviated title (ISO 4)".

Tips for Working with Zotero or Other Citation Managers

• Correct article titles so that only the first word and proper nouns are capitalized.

• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
  • e.g., Escherichia coli to <i>Escherichia coli</i> = Escherichia coli
• To add Greek letters or other symbols, you can also add HTML tags.
  • e.g., beta to &beta; = β
• For citing a publication from a consortium (example R Core team), you can switch the normal First Name MI Last Name formatting by clicking on the rectangular box to with right of the author name.
• Double-check articles with page numbers beginning with 1! This happens when you import a PDF from a digital journal (like mBio or PLoS XXX) that uses article numbers. Fix the starting page to be the article number and delete the ending page so it is blank.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a graphical legend for symbols within a figure, NOT just in the figure caption.
• Don't include the written figure caption in the figure file. Include it in the manuscript.
• Unlike the defaults in Microsoft Excel and/or ggplot2:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs, except major reference lines (e.g., zero, control, or wild-type values for comparison).
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be extremely careful to not change the locations of data points or error bars relative to axis ticks during this process!!)

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform and if you need to change the font of a document. You can generally copy-paste from this table.

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Scientific Conventions

• Use the prime symbol, not a single quote for DNA's 5′ and 3′ ends (see Symbols section above).
• Separate number from units with a space: 200 µL, not 200µL.
• For microbes, gene names are italicized (pykF) and their protein products are capitalized and not italicized (PykF).
• Insertion sequence and transposon names have the IS/Tn in normal font and the following number italicized (IS1, IS150, Tn7).
• Promoter names are often a capital "P" followed by a subscript name of the gene they were taken from (in italics) or a name such as for synthetic promoters from the iGEM registry (not in italics). Less often they are a capital "P" followed by lowercase letters. (Preferred: P_yijC, P_J23100, P_CP25; OK: Ptac).
• Plasmid names should start with a lowercase "p" and then a designation consisting of uppercase letters and numbers. It is best practices for this to be the initials of a researcher or collection followed by a numeric index (pBTK800, pJEB11, pUC19).

Further Reading

• ASM Nomenclature Guidelines - includes information on naming mutations and alleles.

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

! Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and Ethics Program, University of Pittsburgh)

General Formatting

• Manuscripts should generally be double spaced throughout.
• Don't format with multiple columns.
• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
• Don't indent the first paragraph after a heading.
• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• Use Zotero to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• Be sure you are using standard journal abbreviations. You can find them by Googling and looking for: "Abbreviated title (ISO 4)".

Tips for Working with Zotero or Other Citation Managers

• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also uncapitalize words after colons in the title. "This is the title: how to do it". Normal style is to only capitalize the part after a title if it is a complete sentence (independent phrase). "How to write titles: This is how to do it".
• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
  • e.g., Escherichia coli to <i>Escherichia coli</i> = Escherichia coli
• To add Greek letters or other symbols, you can also add HTML tags.
  • e.g., beta to &beta; = β
• For citing a publication from a consortium (example R Core team), you can switch the normal First Name MI Last Name formatting by clicking on the rectangular box to with right of the author name.
• Double-check articles with page numbers beginning with 1! This happens when you import a PDF from a digital journal (like mBio or PLoS XXX) that uses article numbers. Fix the starting page to be the article number and delete the ending page so it is blank.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a graphical legend for symbols within a figure, NOT just in the figure caption.
• Don't include the written figure caption in the figure file. Include it in the manuscript.
• Unlike the defaults in Microsoft Excel and/or ggplot2:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs, except major reference lines (e.g., zero, control, or wild-type values for comparison).
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be extremely careful to not change the locations of data points or error bars relative to axis ticks during this process!!)

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform and if you need to change the font of a document. You can generally copy-paste from this table.

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Scientific Conventions

• Separate number from units with a space: 200 µL, not 200µL.

• Insertion sequence and transposon names have the IS/Tn in normal font and the following number italicized (IS1, IS150, Tn7).
• Promoter names are often a capital "P" followed by a subscript name of the gene they were taken from (in italics) or a name such as for synthetic promoters from the iGEM registry (not in italics). Less often they are a capital "P" followed by lowercase letters. (Preferred: P_yijC, P_J23100, P_CP25; OK: Ptac).
• Plasmid names should start with a lowercase "p" and then a designation consisting of uppercase letters and numbers. It is best practices for this to be the initials of a researcher or collection followed by a numeric index (pBTK800, pJEB11, pUC19).

Further Reading

• ASM Nomenclature Guidelines - includes information on naming mutations and alleles.

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and Ethics Program, University of Pittsburgh)

General Formatting

• Manuscripts should generally be double spaced throughout.
• Don't format with multiple columns.
• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.

• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• Use Zotero to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

Tips for Working with Zotero or Other Citation Managers

• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also uncapitalize words after colons in the title. "This is the title: how to do it". Normal style is to only capitalize the part after a title if it is a complete sentence (independent phrase). "How to write titles: This is how to do it".
• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
  • e.g., Escherichia coli to <i>Escherichia coli</i> = Escherichia coli
• To add Greek letters or other symbols, you can also add HTML tags.
  • e.g., beta to &beta; = β
• For citing a publication from a consortium (example R Core team), you can switch the normal First Name MI Last Name formatting by clicking on the rectangular box to with right of the author name.
• Double-check articles with page numbers beginning with 1! This happens when you import a PDF from a digital journal (like mBio or PLoS XXX) that uses article numbers. Fix the starting page to be the article number and delete the ending page so it is blank.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).

• Unlike the defaults in Microsoft Excel and/or ggplot2:
  • Enclose the data frame of a graph in a full box.

• • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be extremely careful to not change the locations of data points or error bars relative to axis ticks during this process!!)

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform and if you need to change the font of a document. You can generally copy-paste from this table.

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Scientific Conventions

• Separate number from units with a space: 200 µL, not 200µL.
• For microbes, gene names are italicized (lasT) and their protein products are capitalized and not italicized (LasT).
• Insertion sequence and transposon names have the IS/Tn in normal font and the following number italicized (IS1, IS150, Tn7).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and Ethics Program, University of Pittsburgh)

General Formatting

• Manuscripts should generally be double spaced throughout.
• Don't format with multiple columns.
• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• Use Zotero to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

Tips for Working with Zotero or Other Citation Managers

• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also uncapitalize words after colons in the title. "This is the title: how to do it". Normal style is to only capitalize the part after a title if it is a complete sentence (independent phrase). "How to write titles: This is how to do it".
• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
  • e.g., Escherichia coli to <i>Escherichia coli</i> = Escherichia coli
• To add Greek letters or other symbols, you can also add HTML tags.
  • e.g., beta to &beta; = β
• For citing a publication from a consortium (example R Core team), you can switch the normal First Name MI Last Name formatting by clicking on the rectangular box to with right of the author name.
• Double-check articles with page numbers beginning with 1! This happens when you import a PDF from a digital journal (like mBio or PLoS XXX) that uses article numbers. Fix the starting page to be the article number and delete the ending page so it is blank.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel and/or ggplot2:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be extremely careful to not change the locations of data points or error bars relative to axis ticks during this process!!)

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform and if you need to change the font of a document. You can generally copy-paste from this table.

Scientific Conventions

• Use the prime symbol, not a single quote (see above) for DNA's 5′ and 3′ ends.

• For microbes, gene names are italicized (lasT) and their protein products are capitalized and not italicized (LasT).
• Insertion sequence and transposon names have the IS/Tn in normal font and the following number italicized (IS1, IS150, Tn7).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and Ethics Program, University of Pittsburgh)

General Formatting

• Manuscripts should generally be double spaced throughout.
• Don't format with multiple columns.
• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also uncapitalize words after colons in the title. "This is the title: how to do it". Normal style is to only capitalize the part after a title if it is a complete sentence (independent phrase). "How to write titles: This is how to do it".
• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
  • e.g., Escherichia coli to <i>Escherichia coli</i> = Escherichia coli
• To add Greek letters or other symbols, you can also add HTML tags.
  • e.g., beta to &beta; = β

• Double-check articles with page numbers beginning with 1! This happens when you import a PDF from a digital journal (like mBio or PLoS XXX) that uses article numbers. Fix the starting page to be the article number and delete the ending page so it is blank.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.

• • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.

Symbols

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Scientific Conventions

• Use the prime symbol, not a single quote (see above) for DNA's 5′ and 3′ ends.
• For microbes, gene names are italicized (lasT) and their protein products are capitalized and not italicized (LasT).
• Insertion sequence and transposon names have the IS/Tn in normal font and the following number italicized (IS1, IS150, Tn7).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.

• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

Tips for Working with Mendeley

• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the Digital Object Identifier (DOI) and/or the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
  • Annoyingly, you may have to manually correct any cases where the initial "a" is present in an author's name to be uppercase after importing!
• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also uncapitalize words after colons in the title. "This is the title: how to do it". Normal style is to only capitalize the part after a title if it is a complete sentence (independent phrase). "How to write titles: This is how to do it".
• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.

• For citing a publication from a consortium (example R Core team), you can suppress the normal First Name MI Last Name formatting by Mendeley by clicking on the name with (Institution/Organization) after it in the drop-down menu after you enter it in the author box.
• Double-check articles with page numbers beginning with 1! This happens when you import a PDF from a digital journal (like mBio or PLoS XXX) that uses article numbers. Fix the starting page to be the article number and delete the ending page so it is blank.
• You can prevent the HTML links to articles from appearing after each bibliography entry by going to > Citation Style > More Styles and changing the "Include URLs" menu setting.
• To enable using journal abbreviations follow these directions:
  1. Open the Mendeley Desktop user data folder by pressing Cmd+Shift+D (Mac) and clicking 'Open Data Directory'.
  2. Create a folder inside the Data Directory called "journalAbbreviations".
  3. Within this folder, create a plain text file called "default.txt". Each line in this file is a full journal title followed by a tab and then the abbreviation to substitute for this journal title. Matching of the journal title is case-sensitive.
     • You can download a version of this file that should contain most common abbreviations here.
  4. If an entry does not exist in this file, you can find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this table.

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Scientific Conventions

• Use the prime symbol, not a single quote (see above) for DNA's 5′ and 3′ ends.
• For microbes, gene names are italicized (lasT) and their protein products are capitalized and not italicized (LasT).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
• Manuscripts should generally be double spaced throughout.
• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

Tips for Working with Mendeley

• Correct article titles so that only the first word and proper nouns are capitalized.

• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• For citing a publication from a consortium (example R Core team), you can suppress the normal First Name MI Last Name formatting by Mendeley by clicking on the name with (Institution/Organization) after it in the drop-down menu after you enter it in the author box.

• You can prevent the HTML links to articles from appearing after each bibliography entry by going to > Citation Style > More Styles and changing the "Include URLs" menu setting.
• To enable using journal abbreviations follow these directions:
  1. Open the Mendeley Desktop user data folder by pressing Cmd+Shift+D (Mac) and clicking 'Open Data Directory'.
  2. Create a folder inside the Data Directory called "journalAbbreviations".
  3. Within this folder, create a plain text file called "default.txt". Each line in this file is a full journal title followed by a tab and then the abbreviation to substitute for this journal title. Matching of the journal title is case-sensitive.
     • You can download a version of this file that should contain most common abbreviations here.
  4. If an entry does not exist in this file, you can find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this table.

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Scientific Conventions

• Use the prime symbol, not a single quote (see above) for DNA's 5′ and 3′ ends.
• For microbes, gene names are italicized (lasT) and their protein products are capitalized and not italicized (LasT).
• Insertion sequence names have the IS in normal font and the following number italicized (IS1 and IS150).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
• Manuscripts should generally be double spaced throughout.
• Add a page number. Usually centered at the bottom of each page.
• Many journals encourage adding line numbers to aid in review.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

Tips for Working with Mendeley

• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
  • Annoyingly, you will have to manually correct any cases where the initial "a" is present in an author's name to be uppercase after importing!
• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also capitalize words after colons in the title.
• To add italics to species names in downloaded citation titles, add HTML italics tags around them within the Mendeley client. Unfortunately, if you re-edit another part of the citation, the italics are often lost and you will have to go back in and do this again.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• For citing a publication from a consortium (example R Core team), you can suppress the normal First Name MI Last Name formatting by Mendeley by clicking on the name with (Institution/Organization) after it in the drop-down menu after you enter it in the author box.
• You can prevent the HTML links to articles from appearing after each bibliography entry by going to > Citation Style > More Styles and changing the "Include URLs" menu setting.
• To enable using journal abbreviations follow these directions:
  1. Open the Mendeley Desktop user data folder by pressing Cmd+Shift+D (Mac) and clicking 'Open Data Directory'.
  2. Create a folder inside the Data Directory called "journalAbbreviations".
  3. Within this folder, create a plain text file called "default.txt". Each line in this file is a full journal title followed by a tab and then the abbreviation to substitute for this journal title. Matching of the journal title is case-sensitive.
     • You can download a version of this file that should contain most common abbreviations here.
  4. If an entry does not exist in this file, you can find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or R for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this table.

Scientific Conventions

• Use the prime symbol, not a single quote (see above) for DNA's 5′ and 3′ ends.
• For microbes, gene names are italicized (lasT) and their protein products are capitalized and not italicized (LasT).
• Insertion sequence names have the IS in normal font and the following number italicized (IS1 and IS150).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.
• Manuscripts should generally be double spaced throughout.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.

• To enable using journal abbreviations follow these directions:
  1. Open the Mendeley Desktop user data folder by pressing Cmd+Shift+D (Mac) and clicking 'Open Data Directory'.
  2. Create a folder inside the Data Directory called "journalAbbreviations".
  3. Within this folder, create a plain text file called "default.txt". Each line in this file is a full journal title followed by a tab and then the abbreviation to substitute for this journal title. Matching of the journal title is case-sensitive.
     • You can download a version of this file that should contain most common abbreviations here.
  4. If an entry does not exist in this file, you can find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this table.

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Scientific Conventions

• Use the prime symbol, not a single quote (see above) for DNA's 5′ and 3′ ends.
• For microbes, gene names are italicized (lasT) and their protein products are capitalized and not italicized (LasT).
• Insertion sequence names have the IS in normal font and the following number italicized (IS1 and IS150).

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citation titles, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
• To enable using journal abbreviations follow these directions:
  1. Open the Mendeley Desktop user data folder by pressing Cmd+Shift+D (Mac) and clicking 'Open Data Directory'.
  2. Create a folder inside the Data Directory called "journalAbbreviations".
  3. Within this folder, create a plain text file called "default.txt". Each line in this file is a full journal title followed by a tab and then the abbreviation to substitute for this journal title. Matching of the journal title is case-sensitive.
     • You can download a version of this file that should contain most common abbreviations here.
  4. If an entry does not exist in this file, you can find the standard abbreviation using CAS or other resources.
• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also capitalize words after colons in the title.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or other formats for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this table.

Here are some websites that contain many more unicode symbols:
Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citation titles, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.

• Correct article titles so that only the first word and proper nouns are capitalized.
  • Also capitalize words after colons in the title.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or other formats for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Manuscript Style Guide
 

Preferences end here -->

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citation titles, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
• You will generally need to manually correct the journal names from downloaded papers to their standard abbreviations.
  • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or other formats for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this website.

Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions instead of 1/2" indentions to start new paragraphs.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citation titles, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
• You will generally need to manually correct the journal names from downloaded papers to their standard abbreviations.
  • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or other formats for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this website.

Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citation titles, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• If Mendeley fails to automatically detect citation information when you import a PDF or use the Google scholar search by title option, the best way to correct this information without typing it in is to search for the article in PubMed, copy the PubMed ID (PMID) number into the "Catalog IDs" section in Mendeley, and hit the magnifying glass icon.
• You will generally need to manually correct the journal names from downloaded papers to their standard abbreviations.
  • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.
• Neaten up graphs created in Excel or other formats for publication by saving them as PDFs, importing into Adobe Illustrator, and using this to adjust line widths, labels, aspect ratios, add additional details, etc. (Be careful to not change the locations of data points or error bars relative to axis ticks during this process, obviously).

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this website.

Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

General Formatting

• Use a single space after a period between sentences.
• Use 1/4" indentions to start new paragraphs.

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.

• • e.g. Escherichia coli to <i>Escherichia coli</i>

• • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this website.

Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Barrick Lab Style Guide

Writing a Scientific Paper

• Twenty Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176)

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citations, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• You will generally need to manually correct the journal names from downloaded paper to their standard abbreviations.
  • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Create Figures in a vector graphics program (e.g., Adobe Illustrator).
• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.

Symbols

Use Unicode symbols instead of symbol font. They work much better cross-platform. You can generally copy-paste from this website.

Main: Unicode Website | Search
Groups of symbols: Punctuation | Arrows | Math

Barrick Lab Style Guide

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citations, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• You will generally need to manually correct the journal names from downloaded paper to their standard abbreviations.
  • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
  • Do not use shadow effects.
• Use 95% confidence intervals, rather than standard deviations for error bars.

Barrick Lab Style Guide

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citations, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• You will generally need to manually correct the journal names from downloaded paper to their standard abbreviations.
  • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.

• Use 95% confidence intervals, rather than standard deviations for error bars.

Barrick Lab Style Guide

Citations

• Use Mendeley to organize your citations and insert them into word processing documents.
• If you aren't formatting for submission to a specific journal, use the Nature Reviews Genetics style.
• To add italics to species names in downloaded citations, add HTML italics tags around them.
  • e.g. Escherichia coli to <i>Escherichia coli</i>
• You will generally need to manually correct the journal names from downloaded paper to their standard abbreviations.
  • e.g. Journal of Bacteriology to J. Bact.
  • Find the standard abbreviation using CAS or other resources.

Figures and Graphs

• Always include a legend for symbols within a figure, NOT just in the figure caption.
• Unlike the defaults in Microsoft Excel:
  • Enclose the data frame of a graph in a full box.
  • Generally, do not include any grid lines on graphs.
• Use 95% confidence intervals, rather than standard deviations for error bars.